Table 1

Key aspects of HexDiff and other algorithms. The table shows the knowledge used and the parameters required by the different algorithms.

Algorithm

Knowledge Used

Parameters


HexDiff

CRM Locations

Number of hexamers in Hd

Window size

Window score threshold

Ahab

PWMs

Window size

Free energy cutoff

Order of background model

Cluster Buster

PWMs

Motif score threshold

Gap parameter

Cluster score threshold

Residue abundance range

MSCAN

PWMs

Motif score threshold

Window size

Minimum hits

Maximum hits

MCAST

PWMs

Motif score threshold

Maximum allowed distance between adjacent hits

Pseudocount weight

LWF

CRM Locations

String length

Number of mismatches

Detection window size

Maximum number of channels

Channels equalized

Profile cutoff

Peak width cutoff

Smoothing window


Chan and Kibler BMC Bioinformatics 2005 6:262   doi:10.1186/1471-2105-6-262

Open Data